Is the stage downstream known? Are you using the stage as a known water surface boundary condition?
You can compare the known stage-discharge relation to that produced by the model.
You can increase or decrease n-values to allow water to flow less or more freely which will affect the water surface elevation profile produced by the model.
You have to compare the water stage of each cross-section by tuning the Manning's n on one boundary condition set. The modeling water stages should fit to the measured ones. This process calls model calibration. After this process the Manning's n of each cross-section are certain and should not be modified. And then you go on running a different boundary condition set including different flow discharge (upstream BC) and different water stage (downstream BC) with certain Manning's n of each cross-section. You might find that the measured one is a little bit different than the simulated one. This process calls model verification.
Yes I did the same by using the boundary condition (discharge data at the U/S portion and stage data at the D/S portion) but I was unable to calibrate the model. At last I came to know that the stage data at the U/S portion had an error of +/- 10 ft. So, now I hope that is a systematic error coz my model had almost the same error of 5.9 ft every date. Thank you all for your answers!!